Genetic diversity and population structure of <i>Leptosphaeria maculans</i> isolates in Western Canada

Qilin Chen; Gary Peng; Randy Kutcher; Fengqun Yu

doi:10.1016/j.jgg.2021.06.019

Volume 48 Issue 11

Nov. 2021

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Article Navigation > Journal of Genetics and Genomics > 2021 > 48(11): 994-1006

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Genetic diversity and population structure of Leptosphaeria maculans isolates in Western Canada

doi: 10.1016/j.jgg.2021.06.019

a Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada;
b Department of Plant Sciences, Crop Development Centre, University of SK, Saskatoon, SK, Canada

Funds:

We would like to thank Agriculture and Agri-Food Canada for supporting this research.

Received Date: 2021-03-15
Accepted Date: 2021-06-24
Rev Recd Date: 2021-06-17
Publish Date: 2021-11-20

Abstract

Abstract

Leptosphaeria maculans is a serious concern for canola production worldwide. For effective disease management, knowledge of the pathogen's genetic variability and population structure is a prerequisite. In this study, whole-genome sequencing was performed for 162 of 1590 L. maculans isolates collected in the years 2007-2008 and 2012-2014 in Western Canada. DNA variants in genome-wide and specific regions including avirulence (Avr) genes were characterized. A total of 31,870 high-quality polymorphic DNA variants were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants. The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations. Principal component analysis with genome-wide variants showed that the isolates collected in 2012-2014 were more genetically diverse than those collected in 2007-2008. Population structure analysis discovered three distinct sub-populations. Although isolates from Saskatchewan and Alberta were of similar genetic composition, Manitoba isolates were highly diverse. Genome-wide association study detected DNA variants in genes AvrLm4-7, Lema_T86300, and Lema_T86310 associated with the years of collection.
- Leptosphaeria maculans,
- DNA variants,
- Blackleg,
- Genetic diversity,
- Population structure

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References

Alexander, D.H., Novembre, J., Lange, K., 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655-1664.

Ansan-Melayah, D., Balesdent, M.H., Buee, M., Rouxel, T., 1995. Genetic characterization of AvrLm1, the first avirulence gene of Leptosphaeria maculans. Phytopathology 85, 1525-1529.

Balesdent, MH, Barbetti, MJ, Li, H, Sivasithamparam, K, Gout, L, Rouxel, T, 2005. Analysis of Leptosphaeria maculans race structure in a worldwide collection of isolates. Phytopathology 95, 1061-1071.

Balesdent, M.H., Fudal, I., Ollivier, B., Bally, P., Grandaubert, J., Eber, F., Chèvre, A.M., et al., 2013. The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa. New Phytol. 198, 887-898.

Barrins, J.M., Ades, P.K., Salisbury, P.A., Howlett, B.J., 2004. Genetic diversity of Australian isolates of Leptosphaeria maculans, the fungus that causes blackleg of canola (Brassica napus). Austr. Plant Pathol. 33, 529-536.

Barrins, J.M., Purwantara, A., Ades, P.K., Salisbury, P.A., HowlettA, B.J., 2002. Genetic diversity of isolates of Leptosphaeria maculans from a canola (Brassica napus) paddock in Australia. Austr. Plant Pathol. 31, 129-135.

Benjamini, Y., Hochberg, Y., 1995. Controlling the false discovery rate:a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57, 289-300.

Bivand, R., Lewin-Koh, N., 2021. Maptools:Tools for Reading and Handling Spatial Objects. R package version 1.1-1. https://cloud.r-project.org/web/packages/maptools/index.html.

Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y., Buckler, E.S., 2007. TASSEL:software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635.

Burland, T.G., 2020. DNASTAR's Lasergene sequence analysis software. Methods Mol. Biol. 132, 71-91.

Conesa, A., Götz, S., García-Gómez, J.M., Terol, J., Talón, M., Robles, M., 2005. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676.

Copin, R., Wang, X., Louie, E., Escuyer, V., Coscolla, M., Gagneux, S., Palmer, G.H., Ernst, J.D., 2016. Within host evolution selects for a dominant genotype of Mycobacterium tuberculosis while T cells increase pathogen genetic diversity. PLoS Pathog. 12, e1006111.

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., McVean, G., Durbin, R., 2011. The variant call format and VCFtools. Bioinformatics 27, 2156-2158.

Daverdin, G., Rouxel, T., Gout, L., Aubertot, J.N., Fudal, I., Meyer, M., Parlange, F., Carpezat, J., Balesdent, M.H., 2012. Genome structure and reproductive behaviour influence the evolutionary potential of a fungal phytopathogen. PLoS Pathog. 8, e1003020.

Derbyshire, M.C., 2020. Bioinformatic detection of positive selection pressure in plant pathogens:the neutral theory of molecular sequence evolution in action. Front. Microbiol. 11, 644.

Dilmaghani, A., Gladieux, P., Gout, L., Giraud, T., Brunner, P.C., Stachowiak, A., Balesdent, M.H., Rouxel, T., 2012. Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans. Mol. Ecol. 21, 2519-2533.

Dilmaghani, A., Gout, L., Moreno-Rico, O., Dias, J.S., Coudard, L., Castillo-Torres, N., Balesdent, M.H., Rouxel, T., 2013. Clonal populations of Leptosphaeria maculans contaminating cabbage in Mexico. Plant Pathol. 62, 520-532.

Dutreux, F., Da Silva, C., d'Agata, L., Couloux, A., Gay, E.J., Istace, B., Lapalu, N., Lemainque, A., Linglin, J., Noel, B., Wincker, P., 2018. De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing. Sci. Data 5, 1-11.

Frichot, E., François, O., 2015. LEA:an R package for landscape and ecological association studies. Methods Ecol. Evol. 6, 925-929.

Fudal, I., Ross, S., Gout, L., Blaise, F., Kuhn, M., Eckert, M., Cattolico, L., BernardSamain, S., Balesdent, M., Rouxel, T., 2007. Heterochromatin-like regions as ecological niches for avirulence genes in the Leptosphaeria maculans genome:map-based cloning of AvrLm6. Mol. Plant Microbe Interact. 20, 459-470.

Galili, T., 2015. dendextend:an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 31, 3718-3720.

Gauch, H.G., Qian, S., Piepho, H.P., Zhou, L., Chen, R., 2019. Consequences of PCA graphs, SNP codings, and PCA variants for elucidating population structure. PLoS One 14, e0218306.

Gay, E.J., Soyer, J.L., Lapalu, N., Linglin, J., Fudal, I., Da Silva, C., Wincker, P., Aury, J.M., Cruaud, C., Levrel, A., Lemoine, J., 2021. Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. BMC Biol. 19, 1-27.

Gerritsen, H., Gerritsen, M.H., 2017. Package 'mapplots'. http://CRAN.Rproject.org/package=mapplots.

Ghanbarnia, K., Fudal, I., Larkan, N.J., Links, M.G., Balesdent, M.H., Profotova, B., Fernando, W.D.G., Rouxel, T., Borhan, M.H., 2015. Rapid identification of the Leptosphaeria maculans avirulence gene AvrLm2 using an intraspecific comparative genomics approach. Mol. Plant Pathol. 16, 699-709.

Ghanbarnia, K., Ma, L., Larkan, N.J., Haddadi, P., Fernando, D.W.G., Borhan, M.H., 2018. Leptosphaeria maculans AvrLm9:a new player in the game of hide and seek with AvrLm4-7. Mol. Plant Pathol. 19, 1754-1764.

Gout, L., Fudal, I., Kuhn, M.L., Blaise, F., Eckert, M., Cattolico, L., Balesdent, M.H., et al., 2006. Lost in the middle of nowhere:the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans. Mol. Microbiol. 60, 67-80.

Guo, X.W., Fernando, W.G.D., 2005. Seasonal and diurnal patterns of spore dispersal by Leptosphaeria maculans from canola stubble in relation to environmental conditions. Plant Dis. 89, 97-104.

Hayden, H.L., Cozijnsen, A.J., Howlett, B.J., 2007. Microsatellite and minisatellite analysis of Leptosphaeria maculans in Australia reveals regional genetic differentiation. Phytopathology 97, 879-887.

Huang, Y.J., Evans, N., Fitt, B.D., Li, Z.Q., Rouxel, T., Balesdent, M.H., 2013. Fitness cost associated with loss of the AvrLm4 avirulence function in Leptosphaeria maculans (phoma stem canker of oilseed rape). Eur. J. Plant Pathol. 114, 77-89.

Kahle, D., Wickham, H., 2013. ggmap:spatial visualization with ggplot2. R J. 5, 144-161.

Kassambara, A., Mundt, F., 2017. Factoextra:extract and visualize the results of multivariate data analyses. R Pack. Vers. 1, 337-354.

Korunes, K.L., Samuk, K., 2020. pixy:unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Mol. Ecol. Resour. 21, 1359-1368.

Kutcher, H.R., Balesdent, M.H., Rimmer, S.R., Rouxel, T., Chevre, A.M., Delourme, R., Brun, H.J., 2010. Frequency of avirulence genes in Leptosphaeria maculans in Western Canada. Can. J. Plant Pathol. 32, 77-85.

Kutcher, H.R., Cross, D., Nabetani, K., Kirkham, C.L., 2011. A large-scale survey of races of Leptosphaeria maculans occurring on canola in Western Canada. Final report to the canola agronomic research program (carp) 2007-11. https://www.saskcanola.com/quadrant/System/research/reports/Kutcher_CARP_2007-11_Long_Report.pdf.

Lê, S., Josse, J., Husson, F., 2008. FactoMineR:an R package for multivariate analysis. J. Stat. Softw. 25, 1-8.

Li, H., Ruan, J., Durbin, R., 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858.

Li, H., Sivasithamparam, K., Barbetti, M., 2003. Breakdown of a Brassica rapa subsp. sylvestris single dominant blackleg resistance gene in B. napus rapeseed by Leptosphaeria maculans field isolates in Australia. Plant Dis. 87, 752.

Livak, K.J., 1999. Allelic discrimination using fluorogenic probes and the 50 nuclease assay. Genet. Anal. Biomol. Eng. 14, 143-149.

Mahuku, G.S., Goodwin, P.H., Hall, R., Hsiang, T., 1997. Variability in the highly virulent type of Leptosphaeria maculans within and between oilseed rape fields. Can. J. Bot. 75, 1485-1492.

McCarthy, M.I., Abecasis, G.R., Cardon, L.R., Goldstein, D.B., Little, J., Ioannidis, J.P., Hirschhorn, J.N., 2008. Genome-wide association studies for complex traits:consensus, uncertainty and challenges. Nat. Rev. Genet. 9, 356-369.

McDonald, B.A., Linde, C., 2002. The population genetics of plant pathogens and breeding strategies for durable resistance. Euphytica 124, 163-180.

Möller, M., Stukenbrock, E.H., 2017. Evolution and genome architecture in fungal plant pathogens. Nat. Rev. Microbiol. 15, 756-771.

Nei, M., Li, W.H., 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U. S. A. 76, 5269-5273.

Nothnagel, M., Ellinghaus, D., Schreiber, S., Krawczak, M., Franke, A., 2009. A comprehensive evaluation of SNP genotype imputation. Hum. Genet. 125, 163-171.

Parlange, F., Daverdin, G., Fudal, I., Kuhn, M.L., Balesdent, M.H., Blaise, F., GrezesBesset, B., Rouxel, T., 2009. Leptosphaeria maculans avirulence gene AvrLm4-7 confers a dual recognition specificity by the Rlm4 and Rlm7 resistance genes of oilseed rape, and circumvents Rlm4-mediated recognition through a single amino acid change. Mol. Microbiol. 71, 851-863.

Patel, D.A., Zander, M., Van de Wouw, A.P., Mason, A.S., Edwards, D., Batley, J., 2015. Population diversity of Leptosphaeria maculans in Australia. Int. J. Biol. 7, 18-36.

Peluola, C., Fernando, W.G.D., Huvenaars, C., Kutcher, H.R., Lahlali, R., Peng, G., 2013. Effect of flooding on the survival of Leptosphaeria spp. in canola stubble. Plant Pathol. 62, 1350-1356.

Peng, G., Liu, X., McLaren, D.L., McGregor, L., Yu, F., 2020. Seed treatment with the fungicide fluopyram limits cotyledon infection by Leptosphaeria maculans and reduces blackleg of canola. Can. J. Plant Pathol. 2, 1-3.

Petit-Houdenot, Y., Degrave, A., Meyer, M., Blaise, F., Ollivier, B., Marais, C.-L., Jauneau, A., et al., 2019. A two genes-for-one gene interaction between Leptosphaeria maculans and Brassica napus. New Phytol. 223, 397-411.

Plissonneau, C., Blaise, F., Ollivier, B., Leflon, M., Carpezat, J., Rouxel, T., Balesdent, M.H., 2017. Unusual evolutionary mechanisms to escape effectortriggered immunity in the fungal phytopathogen Leptosphaeria maculans. Mol. Ecol. 26, 2183-2198.

Plissonneau, C., Daverdin, G., Ollivier, B., Blaise, F., Degrave, A., Fudal, I., Rouxel, T., Balesdent, M.H., 2016. A game of hide and seek between avirulence genes AvrLm4-7 and AvrLm3 in Leptosphaeria maculans. New Phytol. 209, 1613-1624.

Pritchard, J.K., Stephens, M., Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945-959.

Purwantara, A., Barrins, J., Cozijnsen, A., Ades, P., Howle, B., 2000. Genetic diversity of isolates of the Leptosphaeria maculans species complex from Australia, Europe and North America using amplified fragment length polymorphism analysis. Mycol. Res. 104, 772-781.

Raj, A., Stephens, M., Pritchard, J.K., 2014. fastSTRUCTURE:variational inference of population structure in large SNP data sets. Genetics 197, 573-589.

Roussin, D.M., Binyamin, J., 2018. Historical precipitation characteristics in the Palliser's Triangle region of the Canadian prairies. Prairie Persp. Geogr. Essays 20, 36-48.

Rouxel, T., Balesdent, M.H., 2010. Avirulence genes. eLS. https://doi.org/10.1002/9780470015902.a0021267.

Rouxel, T., Grandaubert, J., Hane, J.K., Hoede, C., Van de Wouw, A.P., Couloux, A., Dominguez, V., Anthouard, V., Bally, P., Bourras, S., 2011. Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeatinduced point mutations. Nat. Commun. 2, 1-10.

Rouxel, T., Penaud, A., Pinochet, X., Brun, H., Gout, L., Delourme, R., Schmit, J., Balesdent, M.H., 2003a. A 10-year survey of populations of Leptosphaeria maculans in France indicates a rapid adaptation towards the Rlm1 resistance gene of oilseed rape. Eur. J. Plant Pathol. 109, 871-881.

Saraçli, S., Doğan, N., Doğan, İ., 2013. Comparison of hierarchical cluster analysis methods by cophenetic correlation. J. Inequal. Appl. 1, 1-8.

Schafer, JL, 1999. Multiple imputation:a primer. Stat. Methods Med. Res. 8, 3-15.

Semagn, K., Babu, R., Hearne, S., Olsen, M., 2014. Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP):overview of the technology and its application in crop improvement. Mol. Breed. 33, 1-14.

Soomro, W., Kutcher, H.R., Yu, F., Hwang, S.F., Fernando, D., Strelkov, S.E., Peng, G., 2020. The race structure of Leptosphaeria maculans in Western Canada between 2012 and 2014 and its influence on blackleg of canola. Can. J. Plant Pathol. 13, 1-14.

Stukenbrock, E.H., Bataillon, T., 2012. A population genomics perspective on the emergence and adaptation of new plant pathogens in agro-ecosystems. PLoS Pathog. 8, e1002893.

Subramanian, A., Subbaraman, N., 2010. Hierarchical cluster analysis of genetic diversity in Maize germplasm. Electron. J. Plant Breed. 1, 431-436.

Tang, W., Wu, T., Ye, J., Sun, J., Jiang, Y., Yu, J., Tang, J., Chen, G., Wang, C., Wan, J., 2016. SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. BMC Plant Biol. 16, 1-11.

Tindall, E.A., Petersen, D.C., Nikolaysen, S., Miller, W., Schuster, S.C., Hayes, V.M., 2010. Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation. BMC Res. Notes 3, 39.

Travadon, R., Sache, I., Dutech, C., Stachowiak, A., Marquer, B., Bousset, L., 2011. Absence of isolation by distance patterns at the regional scale in the fungal plant pathogen Leptosphaeria maculans. Fungal Biol. 115, 649-659.

Van de Wouw, A.P., Lowe, R.G.T., Elliott, C.E., Dubois, D.J., Howlett, B.J., 2014. An avirulence gene, AvrLmJ1, from the blackleg fungus, Leptosphaeria maculans, confers avirulence to Brassica juncea cultivars. Mol. Plant Pathol. 15, 523-530.

Van Inghelandt, D., Melchinger, A.E., Lebreton, C., Stich, B., 2010. Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor. Appl. Genet. 120, 1289-1299.

Velásquez, A.C., Castroverde, C.D.M., He, S.Y., 2018. Plant-pathogen warfare under changing climate conditions. Curr. Biol. 28, R619-R634.

Yu, F., Gugel, R.K., Kutcher, H.R., Peng, G., Rimmer, S.R., 2013. Identification and mapping of a novel blackleg resistance locus LepR4 in the progenies from Brassica napus×B. rapa subsp. sylvestris. Theor. Appl. Genet. 126, 307-315.

Yu, F., Lydiate, D.J., Gugel, R., Sharpe, A., Rimmer, S.R., 2012. Introgression of Brassica rapa subsp. sylvestris blackleg resistance into B. napus. Mol. Breed. 30, 1495-1506.

Zander, M., Patel, D.A., Van de Wouw, A., Lai, K., Lorenc, M.T., Campbell, E., Hayward, A., Edwards, D., Raman, H., Batley, J., 2013. Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. Funct. Integr. Genom. 13, 295-308.

Zhang, X., Fernando, W.G.D., 2018. Insights into Fighting against blackleg disease of Brassica napus in Canada. Crop Pasture Sci. 69, 40-47.

Zhang, X., Peng, G., Kutcher, H.R., Balesdent, M.H., Delourme, R., Fernando, W.G.D., 2016. Breakdown of Rlm3 resistance in the Brassica napusLeptosphaeria maculans pathosystem in western Canada. Eur. J. Plant Pathol. 145, 659-674.

Zou, Z., Liu, F., Fernando, W.D., 2018. Rapid detection of Leptosphaeria maculans avirulence gene AvrLm4-7 conferring the avirulence/virulence specificity on Brassica napus using a tetra-primer ARMS-PCR. Eur. J. Plant Pathol. 152, 515-520.

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